NMR paper Structural heterogeneity in microcrystalline ubiquitin studied by solid-state NMR.

		BioNMR > Educational resources > Journal club
[NMR paper] Structural heterogeneity in microcrystalline ubiquitin studied by solid-state NMR.

Webservers

NMR processing:

MDD

NMR assignment:

Backbone:

Side-chains:

NOEs:

Structure from NMR restraints:

Ab initio:

Fragment-based:

Rosetta-NMR (Robetta)

Template-based:

GeNMR

I-TASSER

Refinement:

Amber

Structure from chemical shifts:

Fragment-based:

Homology-based:

Torsion angles from chemical shifts:

Preditor

TALOS

Promega- Proline

Secondary structure from chemical shifts:

CSI (via RCI server)

TALOS

MICS caps, β-turns

d2D

PECAN

Flexibility from chemical shifts:

RCI

Interactions from chemical shifts:

HADDOCK

Chemical shifts re-referencing:

NMR model quality:

NOEs, other restraints:

Chemical shifts:

RDCs:

Pseudocontact shifts:

Protein geomtery:

SAVES2 or SAVES4

Quality Control Check

NMR spectrum prediction:

FANDAS

MestReS

V-NMR

Flexibility from structure:

Backbone S2

Methyl S2

B-factor

Molecular dynamics:

Gromacs

Amber

Antechamber

Chemical shifts prediction:

From structure:

Shiftx2

Sparta+

Camshift

CH3shift- Methyl

ArShift- Aromatic

ShiftS

Proshift

PPM

CheShift-2- Cα

From sequence:

Shifty

Camcoil

Poulsen_rc_CS

Disordered proteins:

MAXOCC

Format conversion & validation:

CCPN

From NMR-STAR 3.1

Validate NMR-STAR 3.1

NMR sample preparation:

Protein disorder:

DisMeta

Protein solubility:

Isotope labeling:

Solid-state NMR:

Thread Tools

Search this Thread

Rate Thread

Display Modes

02-04-2015, 09:57 PM

nmrlearner

Senior Member

Join Date: Jan 2005

Posts: 23,777

Points: 193,617, Level: 100

Level up: 0%, 0 Points needed

Activity: 50.7%

Last Achievements

Award-Showcase

NMR Credits: 0

NMR Points: 193,617

Downloads: 0

Uploads: 0

Structural heterogeneity in microcrystalline ubiquitin studied by solid-state NMR.

Structural heterogeneity in microcrystalline ubiquitin studied by solid-state NMR.

Related Articles Structural heterogeneity in microcrystalline ubiquitin studied by solid-state NMR.

Protein Sci. 2015 Feb 2;

Authors: Fasshuber HK, Lakomek NA, Habenstein B, Loquet A, Shi C, Giller K, Wolff S, Becker S, Lange A

Abstract
By applying [1-(13) C]- and [2-(13) C]-glucose labeling schemes to the folded globular protein ubiquitin, a strong reduction of spectral crowding and increase in resolution in solid-state NMR (ssNMR) spectra could be achieved. This allowed spectral resonance assignment in a straightforward manner and the collection of a wealth of long-range distance information. A high precision solid-state NMR structure of microcrystalline ubiquitin was calculated with a backbone rmsd of 1.57 to the X-ray structure and 1.32 Å to the solution NMR structure. Interestingly, we can resolve structural heterogeneity as the presence of three slightly different conformations. Structural heterogeneity is most significant for the loop regions ?1-?2 but also for ?-strands ?1, ?2, ?3 and ?5 as well as for the loop connecting ?1 and ?3. This structural polymorphism observed in the solid-state NMR spectra coincides with regions that showed dynamics in solution NMR experiments on different timescales. This article is protected by copyright. All rights reserved.

PMID: 25644665 [PubMed - as supplied by publisher]

More...

Did you find this post helpful?

Similar Threads
Thread	Thread Starter	Forum	Replies	Last Post
Structural heterogeneity in microcrystalline ubiquitin studied by solid-state NMR Structural heterogeneity in microcrystalline ubiquitin studied by solid-state NMR ABSTRACT By applying - and -glucose labeling schemes to the folded globular protein ubiquitin, a strong reduction of spectral crowding and increase in resolution in solid-state NMR (ssNMR) spectra could be achieved. This allowed spectral resonance assignment in a straightforward manner and the collection of a wealth of long-range distance information. A high precision solid-state NMR structure of microcrystalline ubiquitin was calculated with a backbone rmsd of 1.57 to the X-ray structure and 1.32 Å to the...	nmrlearner	Journal club	0	02-02-2015 09:55 PM
[NMR paper] Amplitudes and time scales of picosecond-to-microsecond motion in proteins studied by solid-state NMR: a critical evaluation of experimental approaches and application to crystalline ubiquitin. Amplitudes and time scales of picosecond-to-microsecond motion in proteins studied by solid-state NMR: a critical evaluation of experimental approaches and application to crystalline ubiquitin. http://www.bionmr.com//www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--production.springer.de-OnlineResources-Logos-springerlink.gif Related Articles Amplitudes and time scales of picosecond-to-microsecond motion in proteins studied by solid-state NMR: a critical evaluation of experimental approaches and application to crystalline ubiquitin. J Biomol NMR. 2013 Oct 9; ...	nmrlearner	Journal club	0	10-10-2013 09:38 PM
Structure Calculation from Unambiguous Long-Range Amide and Methyl (1)H-(1)H Distance Restraints for a Microcrystalline Protein with MAS Solid-State NMR Spectroscopy. Structure Calculation from Unambiguous Long-Range Amide and Methyl (1)H-(1)H Distance Restraints for a Microcrystalline Protein with MAS Solid-State NMR Spectroscopy. Structure Calculation from Unambiguous Long-Range Amide and Methyl (1)H-(1)H Distance Restraints for a Microcrystalline Protein with MAS Solid-State NMR Spectroscopy. J Am Chem Soc. 2011 Mar 24; Authors: Linser R, Bardiaux B, Higman V, Fink U, Reif B Magic-angle spinning (MAS) solid-state NMR becomes an increasingly important tool for the determination of structures of membrane...	nmrlearner	Journal club	0	03-26-2011 07:00 PM
[NMR paper] Structural role of tyrosine in Bombyx mori silk fibroin, studied by solid-state NMR a Structural role of tyrosine in Bombyx mori silk fibroin, studied by solid-state NMR and molecular mechanics on a model peptide prepared as silk I and II. Related Articles Structural role of tyrosine in Bombyx mori silk fibroin, studied by solid-state NMR and molecular mechanics on a model peptide prepared as silk I and II. Magn Reson Chem. 2004 Feb;42(2):258-66 Authors: Asakura T, Suita K, Kameda T, Afonin S, Ulrich AS The influence of the bulky and H-bonding Tyr side-chain on its Ala- and Gly-rich environment in Bombyx mori silk fibroin was...	nmrlearner	Journal club	0	11-24-2010 09:25 PM
[NMR paper] Water-protein interactions in microcrystalline crh measured by 1H-13C solid-state NMR Water-protein interactions in microcrystalline crh measured by 1H-13C solid-state NMR spectroscopy. Related Articles Water-protein interactions in microcrystalline crh measured by 1H-13C solid-state NMR spectroscopy. J Am Chem Soc. 2003 Nov 5;125(44):13336-7 Authors: Lesage A, Böckmann A Using solid-state NMR carbon-proton dipolar correlation spectroscopy, we observed hydrogen exchange on the millisecond time scale between water molecules and protein protons in a solid sample. These interactions are shown to be related to important structural...	nmrlearner	Journal club	0	11-24-2010 09:16 PM
Quantitative Analysis of Protein Backbone Dynamics in Microcrystalline Ubiquitin by S Quantitative Analysis of Protein Backbone Dynamics in Microcrystalline Ubiquitin by Solid-State NMR Spectroscopy. Related Articles Quantitative Analysis of Protein Backbone Dynamics in Microcrystalline Ubiquitin by Solid-State NMR Spectroscopy. J Am Chem Soc. 2010 Oct 26; Authors: Schanda P, Meier BH, Ernst M Characterization of protein dynamics by solid-state NMR spectroscopy requires robust and accurate measurement protocols, which are not yet fully developed. In this study, we investigate the backbone dynamics of microcrystalline ubiquitin...	nmrlearner	Journal club	0	10-29-2010 07:05 PM
Quantitative Analysis of Protein Backbone Dynamics in Microcrystalline Ubiquitin by S Quantitative Analysis of Protein Backbone Dynamics in Microcrystalline Ubiquitin by Solid-State NMR Spectroscopy Paul Schanda, Beat H. Meier and Matthias Ernst http://pubs.acs.org/appl/literatum/publisher/achs/journals/content/jacsat/0/jacsat.ahead-of-print/ja100726a/aop/images/medium/ja-2010-00726a_0001.gif Journal of the American Chemical Society DOI: 10.1021/ja100726a http://feeds.feedburner.com/~ff/acs/jacsat?d=yIl2AUoC8zA http://feeds.feedburner.com/~r/acs/jacsat/~4/vMvBmzNs148	nmrlearner	Journal club	0	10-26-2010 08:48 PM
Ubiquitin structure by solid-state NMR Protein Structure Determination by High-Resolution Solid-State NMR Spectroscopy: Application to Microcrystalline Ubiquitin Stephan G. Zech,* A. Joshua Wand, and Ann E. McDermott* http://pubs.acs.org/isubscribe/journals/jacsat/127/i24/figures/ja0503128n00001.gif Contribution from the Department of Chemistry, Columbia University, 3000 Broadway Mail Code 3113, New York, New York 10027, and Department of Biochemistry and Biophysics, University of Pennsylvania, The Johnson Research Foundation, Philadelphia, Pennsylvania 19104 J. Am. Chem. Soc., 127 (24), 8618 -8626, 2005.	nmrlearner	Journal club	0	06-15-2005 07:00 AM

« Previous Thread | Next Thread »

Posting Rules
You may not post new threads You may not post replies You may not post attachments You may not edit your posts BB code is On Smilies are On [IMG] code is On HTML code is On Trackbacks are Off Pingbacks are Off Refbacks are Off